ArticleRNA (New York, N.Y.)2004
Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations.
Article in RNA (New York, N.Y.), 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides.Nucleic acids research · 2022Article
- Computational Modeling of RNA Aptamers: Structure Prediction of the Apo State.The journal of physical chemistry. B · 2022Article
- The Iron Maiden. Cytosolic Aconitase/IRP1 Conformational Transition in the Regulation of Ferritin Translation and Iron Hemostasis.Biomolecules · 2021Article
- Single-molecule fluorescence detection of a tricyclic nucleoside analogue.Chemical science · 2020Article
- Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure.RNA (New York, N.Y.) · 2018Article
- Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy.Nucleic acids research · 2016Article
- Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins.Journal of chemical theory and computation · 2015Article
- Dynamics of riboswitches: Molecular simulations.Biochimica et biophysica acta · 2014Review
- Structural and thermodynamic signatures that define pseudotriloop RNA hairpins.RNA (New York, N.Y.) · 2013Article
- Applying 6-methylisoxanthopterin-enhanced fluorescence to examine protein-DNA interactions in the picomolar range.Biochemistry · 2012Article
- Fe2+ binds iron responsive element-RNA, selectively changing protein-binding affinities and regulating mRNA repression and activation.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Characterization of a K+-induced conformational switch in a human telomeric DNA oligonucleotide using 2-aminopurine fluorescence.Biochemistry · 2010Article
- Dissecting structural transitions in the HIV-1 dimerization initiation site RNA using 2-aminopurine fluorescence.Methods (San Diego, Calif.) · 2009Article
- Fast folding of an RNA tetraloop on a rugged energy landscape detected by a stacking-sensitive probe.Biophysical journal · 2009Article
- RNA folding: conformational statistics, folding kinetics, and ion electrostatics.Annual review of biophysics · 2008Review
- Site-specific variations in RNA folding thermodynamics visualized by 2-aminopurine fluorescence.Biochemistry · 2007Article
- Molecular control of vertebrate iron homeostasis by iron regulatory proteins.Biochimica et biophysica acta · 2006Review
- Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis.Biophysical journal · 2006Article
- Exploring the complex folding kinetics of RNA hairpins: II. Effect of sequence, length, and misfolded states.Biophysical journal · 2006Article
- Solution structure of the apical stem-loop of the human hepatitis B virus encapsidation signal.Nucleic acids research · 2006Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The iron responsive element (IRE) RNA hairpin loop contains six phylogenetically conserved nucleotides, which constitute part of the sequence-specific binding site of the IRE-binding protein. The NMR structure of the loop has been solved, showing that 3 of the 6 nt are poorly constrained. Here, two purine nucleotides in the IRE loop are individually replaced with the fluorescent purine analog 2-aminopurine (2AP). Steady-state and time-resolved fluorescence methods are used to describe the structure and dynamics of 2AP in the IRE loop. The data indicate that 2AP at the position of the adenosine in the loop moves between stacked and unstacked positions, whereas 2AP at the adjacent guanosine is predominantly solvent exposed. Stochastic dynamics simulations are used to provide a physical description of how those nucleotides might move.
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